Package: ECOTOXr 1.1.1

ECOTOXr: Download and Extract Data from US EPA's ECOTOX Database

The US EPA ECOTOX database is a freely available database with a treasure of aquatic and terrestrial ecotoxicological data. As the online search interface doesn't come with an API, this package provides the means to easily access and search the database in R. To this end, all raw tables are downloaded from the EPA website and stored in a local SQLite database <doi:10.1016/j.chemosphere.2024.143078>.

Authors:Pepijn de Vries [aut, cre, dtc]

ECOTOXr_1.1.1.tar.gz
ECOTOXr_1.1.1.zip(r-4.5)ECOTOXr_1.1.1.zip(r-4.4)ECOTOXr_1.1.1.zip(r-4.3)
ECOTOXr_1.1.1.tgz(r-4.4-any)ECOTOXr_1.1.1.tgz(r-4.3-any)
ECOTOXr_1.1.1.tar.gz(r-4.5-noble)ECOTOXr_1.1.1.tar.gz(r-4.4-noble)
ECOTOXr_1.1.1.tgz(r-4.4-emscripten)ECOTOXr_1.1.1.tgz(r-4.3-emscripten)
ECOTOXr.pdf |ECOTOXr.html✨
ECOTOXr/json (API)
NEWS

# Install 'ECOTOXr' in R:

install.packages('ECOTOXr', repos = c('https://pepijn-devries.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/pepijn-devries/ecotoxr/issues

Pkgdown site:https://pepijn-devries.github.io

On CRAN:

4.48 score 10 stars 2 scripts 389 downloads 23 exports 54 dependencies

Last updated 3 months agofrom:44ebd53bbe (on main). Checks:OK: 7. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Dec 01 2024
R-4.5-win	OK	Dec 01 2024
R-4.5-linux	OK	Dec 01 2024
R-4.4-win	OK	Dec 01 2024
R-4.4-mac	OK	Dec 01 2024
R-4.3-win	OK	Dec 01 2024
R-4.3-mac	OK	Dec 01 2024

Exports:as.cas build_ecotox_sqlite cas check_ecotox_availability check_ecotox_build check_ecotox_version cite_ecotox dbConnectEcotox dbDisconnectEcotox download_ecotox_data get_ecotox_info get_ecotox_path get_ecotox_sqlite_file get_ecotox_url is.cas list_ecotox_fields list_ecotox_web_fields search_ecotox search_ecotox_lazy search_query_ecotox show.cas websearch_comptox websearch_ecotox

Dependencies:askpass bit bit64 blob cachem cellranger cli clipr cpp11 crayon curl DBI dbplyr dplyr fansi fastmap generics glue hms httr httr2 jsonlite lifecycle magrittr memoise mime openssl pillar pkgconfig plogr prettyunits progress purrr R6 rappdirs readr readxl rematch rlang RSQLite rvest selectr stringi stringr sys tibble tidyr tidyselect tzdb utf8 vctrs vroom withr xml2

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Build an SQLite database from zip archived tables downloaded from EPA website	build_ecotox_sqlite
Functions for handling chemical abstract service (CAS) registry numbers	as.cas as.character.cas as.data.frame.cas as.double.cas as.integer.cas as.list.cas c.cas cas format.cas is.cas print.cas show.cas [.cas [<-.cas [[.cas [[<-.cas
Check whether a ECOTOX database exists locally	check_ecotox_availability
Check the locally build database for validity	check_ecotox_build
Check if the locally build database is up to date	check_ecotox_version
Cite the downloaded copy of the ECOTOX database	cite_ecotox
Open or close a connection to the local ECOTOX database	dbConnectEcotox dbDisconnectEcotox
Download and extract ECOTOX database files and compose database	download_ecotox_data
Get information on the local ECOTOX database when available	get_ecotox_info
The local path to the ECOTOX database (directory or sqlite file)	get_ecotox_path get_ecotox_sqlite_file
Get ECOTOX download URL from EPA website	get_ecotox_url
List the field names that are available from the ECOTOX database	list_ecotox_fields
Search and retrieve toxicity records from the database	search_ecotox search_ecotox_lazy search_query_ecotox
Search and retrieve substance information from <https://comptox.epa.gov/dashboard>	websearch_comptox
Search and retrieve toxicity records from the on-line database	list_ecotox_web_fields websearch_ecotox